<html><head><base href="x-msg://272/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thanks, I believe this is an important tip.<br><div>
<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Arial; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Arial; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div>Tim</div><br class="Apple-interchange-newline"></span></span>
</div>
<br><div><div>On Dec 8, 2010, at 12:25 AM, Ralf W. Grosse-Kunstleve wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: 'times new roman', 'new york', times, serif; font-size: 10pt; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi Tim,<br><br>If you start from nearly identical copies (due to previous refinement), in the absence of a strong signal from the data, it is expected that the copies remain fairly similar even if you increase the sigma / lower the weight. We just added a new feature to phenix.refine that could be useful to introduce differences between the NCS copies, guided by the model density through a new real-space refinement protocol: strategy=individual_sites_real_space plus real_space_refinement.mode=lockit. At your resolution it is turned on by default. I.e. to try it out all you need to do is get dev-602 or higher and run phenix.refine again. Only trouble, those installers aren't generally visible since there were some minor problems, but watch out for a new one soon.<br><br>Ralf<br><br><br></div><blockquote style="border-left-width: 2px; border-left-style: solid; border-left-color: rgb(16, 16, 255); margin-left: 5px; padding-left: 5px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: 'times new roman', 'new york', times, serif; font-size: 10pt; "><br><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><font face="Tahoma" size="2"><b><span style="font-weight: bold; ">From:</span></b><span class="Apple-converted-space"> </span>Timothy Springer <<a href="mailto:springer@idi.harvard.edu">springer@idi.harvard.edu</a>><br><b><span style="font-weight: bold; ">To:</span></b><span class="Apple-converted-space"> </span><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><b><span style="font-weight: bold; ">Sent:</span></b><span class="Apple-converted-space"> </span>Tue, December 7, 2010 7:31:44 PM<br><b><span style="font-weight: bold; ">Subject:</span></b><span class="Apple-converted-space"> </span>[phenixbb] ncs restraints<br></font><br>Hi, I am using NCS restraints for 4 copies of a molecule at 3.05 �. We are using the standard weights:<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> coordinate_sigma = 0.05</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> b_factor_weight = 10</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">and the 4 molecules look identical. What are suggested values for looser restraints? One of my colleagues said that varying them did not make a difference- ncs was still very strict. Is there a way to make them less strict?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; word-wrap: break-word; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; word-wrap: break-word; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; word-wrap: break-word; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; word-wrap: break-word; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Arial; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Arial; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Arial; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: Arial; ">Timothy A. Springer, Ph.D. </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: Arial; "><span class="Apple-converted-space"></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: Arial; "><font class="Apple-style-span" face="Helvetica"><font class="Apple-style-span" face="Arial"><br></font></font></div></span></span></span></span></div></span></div></span></div></span></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></div><br></div></div></div></blockquote></div>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br></div></span></blockquote></div><br></body></html>